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arXiv math/0610667math.STq-bio.MNstat.APstat.TH
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关于检验基因组的显著性

On testing the significance of sets of genes

Bradley Efron, Robert Tibshirani

摘要:

本文讨论了从微阵列实验中识别差异表达基因组的问题。基因组是外部定义的,例如,来自生物数据库的基因通路组。我们的出发点是Subramanian等人[Proc.Natl. Acad. Sci. USA 102(2005)15545- 15550]。我们研究的问题,在一些一般性,并提出两个潜在的改进GSEA:最大均值统计总结基因集,和更准确的推理重新标准化。我们讨论了各种各样的例子和扩展,包括使用基因集得分的类预测。我们还描述了一个新的R语言包GSA实现我们的想法。

英文摘要:

This paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment. The groups of genes are externally defined, for example, sets of gene pathways derived from biological databases. Our starting point is the interesting Gene Set Enrichment Analysis (GSEA) procedure of Subramanian et al. [Proc. Natl. Acad. Sci. USA 102 (2005) 15545--15550]. We study the problem in some generality and propose two potential improvements to GSEA: the maxmean statistic for summarizing gene-sets, and restandardization for more accurate inferences. We discuss a variety of examples and extensions, including the use of gene-set scores for class predictions. We also describe a new R language package GSA that implements our ideas.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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